1WP5

Crystal structure of the C-terminal domain of DNA topoisomerase IV

Summary for 1WP5

• Entry DOI: 10.2210/pdb1wp5/pdb
• Descriptor: topoisomerase IV (2 entities in total)
• Functional Keywords: broken beta-propeller, hairpin-invaded beta-propeller, six-bladed beta-propeller, isomerase
• Biological source: Geobacillus stearothermophilus
• Total number of polymer chains: 1
• Total formula weight: 37010.91

Authors

Hsieh, T.-J.,Farh, L.,Huang, W.M.,Chan, N.-L. (deposition date: 2004-08-30, release date: 2004-10-12, Last modification date: 2011-07-13)

Primary citation

Hsieh, T.-J.,Farh, L.,Huang, W.M.,Chan, N.-L.
Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis
J.Biol.Chem., 279:55587-55593, 2004

PubMed Abstract: Bacteria possess two closely related yet functionally distinct essential type IIA topoisomerases (Topos). DNA gyrase supports replication and transcription with its unique supercoiling activity, whereas Topo IV preferentially relaxes (+) supercoils and is a decatenating enzyme required for chromosome segregation. Here we report the crystal structure of the C-terminal domain of Topo IV ParC subunit (ParC-CTD) from Bacillus stearothermophilus and provide a structure-based explanation for how Topo IV and DNA gyrase execute distinct activities. Although the topological connectivity of ParC-CTD is similar to the recently determined CTD structure of DNA gyrase GyrA subunit (GyrA-CTD), ParC-CTD surprisingly folds as a previously unseen broken form of a six-bladed beta-propeller. Propeller breakage is due to the absence of a DNA gyrase-specific GyrA box motif, resulting in the reduction of curvature of the proposed DNA binding region, which explains why ParC-CTD is less efficient than GyrA-CTD in mediating DNA bending, a difference that leads to divergent activities of the two homologous enzymes. Moreover, we found that the topology of the propeller blades observed in ParC-CTD and GyrA-CTD can be achieved from a concerted beta-hairpin invasion-induced fold change event of a canonical six-bladed beta-propeller; hence, we proposed to name this new fold as "hairpin-invaded beta-propeller" to highlight the high degree of similarity and a potential evolutionary linkage between them. The possible role of ParC-CTD as a geometry facilitator during various catalytic events and the evolutionary relationships between prokaryotic type IIA Topos have also been discussed according to these new structural insights.

PubMed: 15466871
DOI: 10.1074/jbc.M408934200

Experimental method

X-RAY DIFFRACTION (1.79 Å)